The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Commentaires: 14 pages, 7 figures, submitted

Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component machinery, fueled by adenosine triphosphate, called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation, and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a nonlinear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and traveling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

A method is proposed to generate and study the dynamics of spatial light solitons in a birefringent medium with quadratic nonlinearity. Although no analytical expression for propagating solitons has been obtained, our numerical simulations show the existence of stable localized spatial solitons in the frequency forbidden band gap of the medium. The dynamics of these objects is quite rich and manifests for instance elastic reflections, or inelastic collisions where two solitons merge and propagate as a single solitary wave. We derive the dynamics of the slowly varying envelopes of the three fields (second harmonic pump and two-component signal) and study this new system theoretically. We show that it does present a threshold for nonlinear supratransmission that can be calculated from a series expansion approach with a very high accuracy. Specific physical implications of our theoretical predictions are illustrated on LiGaTe2 (LGT) crystals. Once irradiated by a cw laser beam of 10 mu m wavelength, at an incidence beyond the extinction angle, such crystals will transmit light, in the form of spatial solitons generated in the nonlinear regime above the nonlinear supratransmission threshold.